CCN Synthesis Report

Introduction

The CCN clearinghouse provides a synthesized and curated set of coastal carbon data that promotes the sharing of open data, novel analyses, and collaboration opportunities. The synthesis is created by curating and merging publicly available data through an automated script. This report documents the success or failure of the automated synthesis process, documents changes, conducts QA/QC tests, and provides visualizations and summaries of data within the clearinghouse.

Report date: 2024/07/01-17:52

Synthesis status: Successful

Contact: Jaxine Wolfe (wolfejax@si.edu)

Database Overview

Currently, this synthesis contains 536 studies with soil carbon associated observations across 3981 sites and 15265 cores from around the world. Observations represent a 62 year timespan, from 1960 to 2022.

QA/QC

Test Results Overview

Relational Tables

Cases where a core ID is present in the core-level table but not the depthseries.

Cases where a core ID is present in the depthseries table but not the core-level table.

Uncontrolled Attributes

The studies with uncontrolled attributes in essential tables are the following:

This table provides a more detailed breakdown of these attributes and the values associated with them:

Uncontrolled Variables

uc_vars <- str_split(toString(
  qa_results %>% 
    filter(grepl("Undefined variables", result)) %>% 
    mutate(result = gsub("Undefined variables: ", "", result)) %>% 
    pull(result)), 
  pattern = ", ")[[1]]

# use this table as a hack while I work on a better solution
uncontrolled <- read_csv("docs/resolve_uncontrolled.csv") %>% 
  filter(variable_name %in% uc_vars) %>% 
  filter(attribute_name != "coring_method") %>% 
  select(-c(action, definition, notes, uncontrolled_type)) %>% 
  bind_rows(ccrcn_synthesis$methods %>% 
              filter(coring_method %in% uc_vars) %>% select(study_id, coring_method) %>% 
              rename(variable_name = coring_method) %>% 
              mutate(table_name = "methods", attribute_name = "coring_method")) %>% 
  distinct() %>% arrange(study_id)
# theres a few that aren't included, but it's better than nothin

datatable(uncontrolled,
                    options = list(searching = TRUE,
                         paging = FALSE,
                         info = FALSE,
                         scrollY = 300,
                         scrollX = 300,
                         scrollCollapse = TRUE),
          rownames = FALSE)

Numeric Attributes

Summary Statistics:

Bibliography

Stats and Visualization

Habitats

The following table shows which cores are currently not assigned any habitat:

Geography

The following table shows which cores are currently not assigned any country. This may be because the latitude and longitude are undefined.

Depthseries

Depth Interval Checks

The following studies have cores with a max depth of NA or 0: Nahlik_and_Fennessy_2016, Mbense_et_al_2016, Langston_et_al_2022, Agawin_et_al_1996, De_Iongh_et_al_1995, Holmer_et_al_2007, Townsend_and_Fonseca_1998, Van_Engeland_2010

Instances of multiple observations for the same interval within a unique core (and unique method ID) were found in the following 44 studies:

Boyd_et_al_2017, Buffington_et_al_2020, Callaway_et_al_2019, CRMS_Database, Drexler_et_al_2009, Drexler_et_al_2013, Everhart_et_al_2020, Fourqurean_and_Kendrick_unpublished, Geldenhyus_et_al_2016, Gerlach_et_al_2017, Gonneea_et_al_2004, Howard_and_Fourqurean_2020, Human_et_al_2022, Johnson_et_al_2020, Johnson_et_al_2024_eelgrass, Kemp_et_al_2020, Kemp_et_al_2023, Kemp_et_al_2024, Kumar_et_al_2020, Langston_et_al_2022, MacKenzie_et_al_2021, Marot_et_al_2020, Mbense_et_al_2016, Messerschmidt_and_Kirwan_2020, Nahlik_and_Fennessy_2016, NCSS, Oakes_and_Connolly_2004, Orson_1990, Paula_et_al_2001, Peer_et_al_2018, Quafisi_et_al_2024, Rajkaran_and_Adams_2011, Rigollet_et_al_2004, Schieder_and_Kirwan_2019, Smeaton_et_al_2022b, Smeaton_et_al_2023, Stahl_et_al_2024, StLaurent_et_al_2020, Strand_et_al_2024, Trettin_et_al_2017, Tully_et_al_2024, Van_de_Broek_et_al_2018, Wang_et_al_2023, Watson_and_Byrne_2013

There are 4228 single-interval surface samples (max depth < 20cm) and 179 single-interval subsurface samples. There are also 644 large single-interval samples (ex. one representative (?) sample for 0-100cm depth).

The following 3 studies had at least one depth interval where the depth max was less than the depth min: Bezuidenhout_et_al_2011, DelVecchia_et_al_2014, Thom_1992

Numeric Data Distributions

Relationship between organic matter (LOI) and carbon content

Change Log

COMING SOON

The following table summarizes which entries across the range of synthesis tables changed compared to the previous synthesis. Study IDs associated with the “forward” change type represent data that was not present in the previous synthesis, while “backward” indicates that study ID is no longer in the given table. If a study ID in a table is associated with both backward and forward change types, it is likely that one or more values were altered for that row in the new synthesis.

Miscellaneous

The following files were found in the derivative folders. They either do not match the approved filename structure for csvs or are another filetype

Unknown CSVs

##  [1] "data/primary_studies/Adotey_et_al_2024/derivative/Adotey_et_al_2024_allometric_eq.csv"          
##  [2] "data/primary_studies/Adotey_et_al_2024/derivative/Adotey_et_al_2024_plant.csv"                  
##  [3] "data/primary_studies/Adotey_et_al_2024/derivative/Adotey_et_al_2024_plot_summary.csv"           
##  [4] "data/primary_studies/CIFOR/derivative_ALT/cifor_alt_allometric_eq.csv"                          
##  [5] "data/primary_studies/CIFOR/derivative_ALT/cifor_alt_plant_plot_summary.csv"                     
##  [6] "data/primary_studies/CIFOR/derivative_ALT/cifor_alt_plant.csv"                                  
##  [7] "data/primary_studies/CIFOR/derivative_ALT/cifor_alt_plot_summary.csv"                           
##  [8] "data/primary_studies/CIFOR/derivative_SWAMP/cifor_swamp_allometric_eq.csv"                      
##  [9] "data/primary_studies/CIFOR/derivative_SWAMP/cifor_swamp_plants.csv"                             
## [10] "data/primary_studies/CIFOR/derivative_SWAMP/cifor_swamp_plots.csv"                              
## [11] "data/primary_studies/Craft_2024/derivative/Craft_2024_associated_publication.csv"               
## [12] "data/primary_studies/Dontis_et_al_2020/derivative/Dontis_et_al_2020_allometric_eq.csv"          
## [13] "data/primary_studies/Dontis_et_al_2020/derivative/Dontis_et_al_2020_plant.csv"                  
## [14] "data/primary_studies/Dontis_et_al_2020/derivative/Dontis_et_al_2020_plot_summary.csv"           
## [15] "data/primary_studies/Fourqurean_2012/derivative/Fourqurean_2012_biomass.csv"                    
## [16] "data/primary_studies/Gillen_et_al_2018/derivative/Gillen_et_al_2018_plant_plot_detail.csv"      
## [17] "data/primary_studies/Gillen_et_al_2018/derivative/Gillen_et_al_2018_plot_summary.csv"           
## [18] "data/primary_studies/Johnson_et_al_2024_seagrass/derivative/Johnson_et_al_2024_eelgrass.csv"    
## [19] "data/primary_studies/Morgan_et_al_2024/derivative/morgan_et_al_2024_plot_summary.csv"           
## [20] "data/primary_studies/Radabaugh_et_al_2017/derivative/radabaugh_et_al_2017_allometric_eq.csv"    
## [21] "data/primary_studies/Radabaugh_et_al_2017/derivative/radabaugh_et_al_2017_plant_plot_detail.csv"
## [22] "data/primary_studies/Radabaugh_et_al_2017/derivative/radabaugh_et_al_2017_plant.csv"            
## [23] "data/primary_studies/Radabaugh_et_al_2017/derivative/radabaugh_et_al_2017_plot_summary.csv"     
## [24] "data/primary_studies/Radabaugh_et_al_2018/derivative/radabaugh_et_al_2018_plot_summary.csv"     
## [25] "data/primary_studies/Radabaugh_et_al_2023/derivative/radabaugh_et_al_2023_allometric_eq.csv"    
## [26] "data/primary_studies/Radabaugh_et_al_2023/derivative/radabaugh_et_al_2023_plant.csv"            
## [27] "data/primary_studies/Radabaugh_et_al_2023/derivative/radabaugh_et_al_2023_plot_summary.csv"     
## [28] "data/primary_studies/Simard_et_al_2019/derivative/Simard_et_al_2019_plant_plot_detail.csv"      
## [29] "data/primary_studies/Simard_et_al_2019/derivative/Simard_et_al_2019_plant.csv"                  
## [30] "data/primary_studies/Simard_et_al_2019/derivative/Simard_et_al_2019_plot_summary.csv"           
## [31] "data/primary_studies/Trettin_et_al_2020/derivative/trettin_et_al_2020_study_citation.csv"

Non .csv or .bib filetypes

##  [1] "data/primary_studies/Brown_et_al_2024/derivative/_readMe.txt"          
##  [2] "data/primary_studies/Darienzo_and_Peterson_1990/derivative/_readMe.rtf"
##  [3] "data/primary_studies/Dontis_et_al_2020/derivative/_readMe.txt"         
##  [4] "data/primary_studies/Everhart_et_al_2020/derivative/_readMe.txt"       
##  [5] "data/primary_studies/Gillen_et_al_2018/derivative/_readMe.txt"         
##  [6] "data/primary_studies/Langston_et_al_2022/derivative/_readMe.txt"       
##  [7] "data/primary_studies/Messerschmidt_et_al_2020/derivative/_readMe.txt"  
##  [8] "data/primary_studies/Morgan_et_al_2024/derivative/_readMe.rtf"         
##  [9] "data/primary_studies/Radabaugh_et_al_2017/derivative/_readMe.txt"      
## [10] "data/primary_studies/Radabaugh_et_al_2018/derivative/_readMe.txt"      
## [11] "data/primary_studies/Radabaugh_et_al_2021/derivative/_readMe.txt"      
## [12] "data/primary_studies/Radabaugh_et_al_2023/derivative/_readMe.txt"      
## [13] "data/primary_studies/Simard_et_al_2019/derivative/_readMe.rtf"         
## [14] "data/primary_studies/Smith_and_Kirwan_2021/derivative/_readMe.txt"     
## [15] "data/primary_studies/Stevens_et_al_2024/derivative/_readMe.txt"        
## [16] "data/primary_studies/Vinent_and_Kirwan_2017/derivative/_readMe.txt"

Warnings Encountered

## 1 identical warnings:
## In left_join(., study_site_core) :
##   [38;5;232mEach row in `x` is expected to match at most 1 row in `y`.
## [36mℹ[38;5;232m Row 702 of `x` matches multiple rows.
## [36mℹ[38;5;232m If multiple matches are expected, set `multiple = "all"` to silence this warning.[39m